Dear All, After coot rebuid,Igot a protein 3-D structure, and Phenix comprehensive validation demonstrated it is almost acceptable.Then I did the Phenix refinement , and I select all the strategies which suitable for my resolution, all the restraints and weights (default choice) suitable for my resolution, all the other options suitable for me. I optimized it 10 rounds.However after I got the PDB output file and the mtz output file after refinment, analysis by Phenix comprehensive validation demonstrated the quality of the quality of the protein 3-D structure has been lowered significantly, which makes it unacceptable. Will you please tell me how to process my refinement? In Phenix refine, which kinds of combination of strategy combination are allowable, which are not allowable, which kinds of combination of restraints and weight combination are allowable, which are not allowable, which kinds of combinations of option are allowable, which are not allowable, and why? I am looking forward to getting your reply. Cheers, Dialing